Job ID = 6456215 SRX = SRX331372 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:43:53 prefetch.2.10.7: 1) Downloading 'SRR947609'... 2020-06-21T10:43:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:46:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:46:36 prefetch.2.10.7: 'SRR947609' is valid 2020-06-21T10:46:36 prefetch.2.10.7: 1) 'SRR947609' was downloaded successfully Read 13556446 spots for SRR947609/SRR947609.sra Written 13556446 spots for SRR947609/SRR947609.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:06 13556446 reads; of these: 13556446 (100.00%) were unpaired; of these: 901265 (6.65%) aligned 0 times 11950633 (88.15%) aligned exactly 1 time 704548 (5.20%) aligned >1 times 93.35% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1683818 / 12655181 = 0.1331 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:54:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:54:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:21: 1000000 INFO @ Sun, 21 Jun 2020 19:54:27: 2000000 INFO @ Sun, 21 Jun 2020 19:54:33: 3000000 INFO @ Sun, 21 Jun 2020 19:54:39: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:54:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:45: 5000000 INFO @ Sun, 21 Jun 2020 19:54:50: 1000000 INFO @ Sun, 21 Jun 2020 19:54:51: 6000000 INFO @ Sun, 21 Jun 2020 19:54:56: 2000000 INFO @ Sun, 21 Jun 2020 19:54:58: 7000000 INFO @ Sun, 21 Jun 2020 19:55:02: 3000000 INFO @ Sun, 21 Jun 2020 19:55:05: 8000000 INFO @ Sun, 21 Jun 2020 19:55:08: 4000000 INFO @ Sun, 21 Jun 2020 19:55:12: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:55:13: 5000000 INFO @ Sun, 21 Jun 2020 19:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:55:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:55:19: 10000000 INFO @ Sun, 21 Jun 2020 19:55:19: 6000000 INFO @ Sun, 21 Jun 2020 19:55:21: 1000000 INFO @ Sun, 21 Jun 2020 19:55:25: 7000000 INFO @ Sun, 21 Jun 2020 19:55:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:55:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:55:26: #1 total tags in treatment: 10971363 INFO @ Sun, 21 Jun 2020 19:55:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:55:26: #1 tags after filtering in treatment: 10971149 INFO @ Sun, 21 Jun 2020 19:55:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:27: 2000000 INFO @ Sun, 21 Jun 2020 19:55:27: #2 number of paired peaks: 4987 INFO @ Sun, 21 Jun 2020 19:55:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:27: #2 predicted fragment length is 226 bps INFO @ Sun, 21 Jun 2020 19:55:27: #2 alternative fragment length(s) may be 226 bps INFO @ Sun, 21 Jun 2020 19:55:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.05_model.r INFO @ Sun, 21 Jun 2020 19:55:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:30: 8000000 INFO @ Sun, 21 Jun 2020 19:55:33: 3000000 INFO @ Sun, 21 Jun 2020 19:55:36: 9000000 INFO @ Sun, 21 Jun 2020 19:55:39: 4000000 INFO @ Sun, 21 Jun 2020 19:55:42: 10000000 INFO @ Sun, 21 Jun 2020 19:55:44: 5000000 INFO @ Sun, 21 Jun 2020 19:55:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:55:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:55:48: #1 total tags in treatment: 10971363 INFO @ Sun, 21 Jun 2020 19:55:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:55:48: #1 tags after filtering in treatment: 10971149 INFO @ Sun, 21 Jun 2020 19:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:49: #2 number of paired peaks: 4987 INFO @ Sun, 21 Jun 2020 19:55:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:49: #2 predicted fragment length is 226 bps INFO @ Sun, 21 Jun 2020 19:55:49: #2 alternative fragment length(s) may be 226 bps INFO @ Sun, 21 Jun 2020 19:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.10_model.r INFO @ Sun, 21 Jun 2020 19:55:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:50: 6000000 INFO @ Sun, 21 Jun 2020 19:55:56: 7000000 INFO @ Sun, 21 Jun 2020 19:56:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:02: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:56:07: 9000000 INFO @ Sun, 21 Jun 2020 19:56:13: 10000000 INFO @ Sun, 21 Jun 2020 19:56:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:56:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:56:19: #1 total tags in treatment: 10971363 INFO @ Sun, 21 Jun 2020 19:56:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:56:20: #1 tags after filtering in treatment: 10971149 INFO @ Sun, 21 Jun 2020 19:56:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.05_summits.bed INFO @ Sun, 21 Jun 2020 19:56:20: Done! pass1 - making usageList (73 chroms): 2 millis pass2 - checking and writing primary data (7806 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:56:21: #2 number of paired peaks: 4987 INFO @ Sun, 21 Jun 2020 19:56:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:21: #2 predicted fragment length is 226 bps INFO @ Sun, 21 Jun 2020 19:56:21: #2 alternative fragment length(s) may be 226 bps INFO @ Sun, 21 Jun 2020 19:56:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.20_model.r INFO @ Sun, 21 Jun 2020 19:56:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:56:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.10_summits.bed INFO @ Sun, 21 Jun 2020 19:56:39: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (4909 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:56:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331372/SRX331372.20_summits.bed INFO @ Sun, 21 Jun 2020 19:57:12: Done! pass1 - making usageList (28 chroms): 2 millis pass2 - checking and writing primary data (2490 records, 4 fields): 5 millis CompletedMACS2peakCalling